Fix symmetry before retopology
Try this:


This will almost certainly screw up your Multires modifier, so apply it.
Select a vertex on the one half—say the left one—and hit Ctrl+L to select everything connected to it.
Delete it with X.
Move the boundary of the top section to align with the Z-axis.


You can try SX0 and then setting X to 0 in the transform properties, you'll probably still have some cleanup to do even if you use proportional editing.

Go out of edit mode and use a mirror modifier. (If I remember correctly, there's a Remove Doubles option you should use.)